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264 protocols using irdye 680

1

Investigating Neuroinflammatory Signaling Pathways

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AlloP (3α-hydroxy-5α-pregnan-20-one) was purchased from Steraloids, Inc. (Newport, RI). AlloP was reconstituted in 22.5% (w/v) 2-hydroxypropyl-β-cyclodextrin, purchased from Sigma (St. Louis, MO). Soluble membrane glycoprotein (gp)130 (sgp130) was purchased from R&D Systems (#468-MG) and reconstituted in vehicle (0.1% BSA in saline) as described previously (14 (link)). For intracerebroventricular injections of IL-6 and sgp130, 1.4 μg was dissolved in 100 μl of vehicle to deliver 100 ng per day via a 14 day osmotic pump, at a pump rate of 0.25 μl per hour (Alzet, mini-osmotic pump, model 1002). BSA (0.1%) in saline was used as the vehicle control for both the sgp130 and IL-6 intracerebroventricular injection studies. IL-6 was purchased from Invitrogen and reconstituted in the vehicle (0.1% BSA in saline). Primary antibodies used for immunoblot analysis included NeuN, Calnexin (Millipore), and Cox 4 (Invitrogen), as well as p-STAT3 and STAT3 (Cell Signaling). Secondary antibodies used included goat anti-mouse IRDye 800 and IRDye 680 (LI-COR) and goat anti-rabbit IRDye 800 and IRDye 680 (LI-COR).
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2

Protein Extraction and Immunoblotting from Adipose and Liver Tissues

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White adipose tissue was homogenized in homogenization buffer (150mM NaCl, 10mM Tris-HCl, 2mM EDTA, pH 7,4) and liver tissue in RIPA-buffer (Radioimmunoprecipitation assay buffer 150 mM NaCl, 2mM EDTA, 0,35% Na-deoxycholate, 0,50% Nonidet-40, 0,10% SDS both buffers were supplied with complete protease inhibitor (Sigma-Aldrich, Merk KGaA, Darmstadt, Germany) and phosphoSTOP (Sigma-Aldrich) using a Teflon douncer or a bead beater. Samples were incubated on ice for 30 min and further centrifuged at 10 000xg for 10 min at 4°C and the supernatants were collected.
Total protein concentration was determined using Bradford assay (BioRad). Total proteins were separated using 10 or 12% gradient SDS-polyacrylamide gel (BioRad) under denaturing conditions. Proteins were transferred onto nitrocellulose filters (Nitropure), and blots were probed with antibodies against phosphorylated and total HSL, GAPDH, ASCL1 (Cell Signaling Technology, Inc, Danvers, MA, USA) and FATP2 (abcam, Cambridge, UK), followed by detection by IRDyeTM 800 anti-Goat IgG and IRDyeTM 680 anti-Rabbit IgG antibodies using The Odyssey® Imaging System (LICOR).
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3

Western Blot Analysis of UCP1 in Brown Adipocytes

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Primary brown adipocytes were lysed in RIPA buffer for western blot analysis. 30 μg of total lysates were separated by SDS-PAGE (12.5% gels), transferred to Odyssey® nitrocellulose membrane (Millipore), and probed with anti-UCP1 (1:10,000; ab10983, Abcam), and anti-Actin (1:10,000; MAB1501, Millipore). Secondary antibodies conjugated to IRDyeTM 680 or IRDyeTM 800 (Licor Biosciences) were incubated at a dilution of 1:20,000. Fluorescent images were captured by Odyssey infrared imaging system (Licor Biosciences).
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4

Immunoblotting Muscle Protein Expression

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Immunoblots were performed as previously described.13 Homogenized tibialis anterior (TA) or soleus (20 μg per well) were separated and transferred to PVDF membranes (Millipore). Membranes were incubated with primary antibodies: phospho‐p38 MAPK (#9211, Thr180/Tyr182, Cell Signaling), p38 MAPK (#9212, Cell Signaling), RyR1 (#ab2868), CSQ1,2 (#ab3516), and DHPR (#ab2864) and thereafter with infrared‐labelled secondary antibodies (IRDye 680, IRDye 800, LI‐COR Biosciences). Detection and analyses were performed with the LI‐COR imaging system and normalized to total protein, which was determined by Ponceau S or Coomassie staining.
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5

Generating IQGAP1 Knockout NIH 3T3 Cells

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A pooled CRISPR knockout line and comparable wild-type NIH 3T3 cells expressing endogenous IQGAP1 were purchased from Synthego (Redwood City, CA). Cells were grown in DMEM (Gibco, Grand Island, NY) supplemented with 10% FBS (Genesee Scientific, San Diego, CA), 200 mM L-glutamine (Gibco), and 45 U/mL penicillin-streptomycin (Gibco). All cell lines were screened for mycoplasma at regular intervals by screening fixed cells for irregular DAPI stain. Clonal lines were produced via dilution by plating 0.5 cells per 48-well plate (Genesee Scientific) and visual confirmation of single-cell deposition. Wells containing cells were grown in conditioned media, grown to ~ 70% confluency, and screened for protein levels via Western blots with monoclonal mouse anti-IQGAP1 (1:1000; 610612, BD Biosciences, East Rutherford, NJ), polyclonal rabbit α-tubulin (1:2500; ab18251, Abcam Inc, Cambridge, United Kingdom), and appropriate secondary antibodies (1:5000 IR-dye-680 for IQGAP1 and IR-dye-800 for α-tubulin; LI-COR Biotechnology, Lincoln, NE). Blots were imaged with a LI-COR Odyssey Fc imaging system (LI-COR Biotechnology).
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6

Tau Protein Expression Analysis

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We used 12% sodium dodecyl sulfate (SDS) polyacrylamide gels to separate 5 µg of total protein from hTau40- and pcDNA3.2-transfected SH-SY5Y differentiated cells before transferring them onto a PVDF (polyvinylidene fluoride) membrane. A tau protein ladder (rPeptide, Watkinsville, GA USA) containing all 6 human isoforms of tau and a recombinant tau 441 (hTau40) protein (rPeptide) were also loaded on the gel as controls. PVDF membranes were blocked for 1 h using Intercept® Blocking Buffer TBS (LI-COR Biosciences) and probed overnight at 4 °C with anti-phospho-Tau (Threonine 181) and anti-total Tau (Tau 12) antibodies at a 1:1000 dilution overnight at 4 °C. Membranes were then incubated with secondary antibody (either IRDye® 680 or IRDye® 800CW) at a 1:10,000 dilution for 1 h at room temperature and scanned using the Odyssey Infrared Imaging System (LI-COR Biosciences).
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7

Tc85-11 Binding to Cytoskeletal Proteins

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Cytokeratins or vimentin were immobilized on 96-wells microtiter plates (200 ng in 50 μl of PBS) (4°C, overnight), blocked with Odyssey blocking buffer for 1h at 37°C and incubated with Tc85-11LamG recombinant protein in PBS (60 μg/ml). Wells were then washed 3 times with PBS and bound protein detected using an anti-gp85 monoclonal antibody (G1G8, kindly provided by Dr. Eliciane Mattos), followed by anti-mouse immunoglobulin-Ig antibodies conjugated with IRDye680 (LI-COR Biosciences). Plates were then analyzed with the Odyssey Imaging System (LI-COR Biosciences). The monoclonal antibody G1G8 recognizes a neutralizing epitope (sequence TGETPLEPFGFCFGA) within the LamG domain of the Tc85-11 protein [14 (link)]. For the competition experiments, the Tc85-11LamG recombinant protein in PBS (60 μg/ml) was incubated in the absence or presence of peptides (200 μM).
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8

Western Blot Antibody Validation

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Sources of primary antibodies were as follows: DNMT3A (2160), DNMT3B (67259), and DNMT1 (5032) were from Cell Signaling Technology (Danvers, MA); AUF1 (sc-166577) and HuR (sc-5261) were from Santa Cruz Biotechnology (Dallas, TX); and GAPDH was from Protein Tech (Chicago, IL, USA). Secondary antibodies conjugated with IRDye 800CW or IRDye 680 were purchased from LI-COR Biosciences (Lincoln, NE). PCR primers (Table S1) were purchased from Integrated DNA Technologies (Coralville, IA).
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9

SDS-PAGE and Western Blot Analysis of U-Omp19

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U-Omp19 samples were run under both non-reducing and reducing conditions by SDS-PAGE as described previously [18] (link). For WB, after being subjected to SDS-PAGE, samples were transferred onto a nitrocellulose membrane. A polyclonal rabbit anti-U-Omp19 serum followed by anti-rabbit IgG labeled with IRDye 680 (LI-COR Biosciences) were used to visualize the bands. Images were captured and documented with an Odyssey infrared image-scanner (LI-COR Biosciences).
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10

Quantifying AMPK, p21, and p27 Protein Levels

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Western blot analysis of experimental and control cell lysates was carried out using the Odyssey® Infrared System (LI-COR Biosciences, Lincoln, NE) and polyclonal anti-phospho-AMPK-α (Thr 172) antibody (Cat # 07-681SP), polyclonal Anti-p21 antibody (Cat # 0506550), and polyclonal Anti-Kip1 (p27) (Cat # 060445) were purchased from Millipore (Millipore Corporation, Iselin, NJ ). Polyclonal beta actin antibody (Cat # sc-1615) and polyclonal RASSF1C antibody (sc-18724) were purchased from Santa Cruz Biotechnology, Inc (Santa Cruz, CA), and fluorescently-labeled secondary antibodies IRDye® 680 and 780 RD Infrared Dye were purchased from LI-COR (LI-COR Biosciences, Lincoln, NE). The experiments were repeated at least 3 times. Protein levels were normalized to actin levels (the loading control).
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